% This code calculates the input resistance for a FS neuron in a
% population, where each neuron has nAvgGJ number of gap junctions.
%
%
% This code calculates the input resistance for a FS neuron in a
% population, where each neuron has nAvgGJ number of gap junctions.
%
%
% Run the following script to generate the data:
%
% calcInputResistance.m
% calcInputResistanceSecDend.m
%
% First parse and plot the figures:
%
% plotInputResistance.m
% plotInputResistanceSecDend.m
%
% After the pre-parsing, a merged figure can be plotted (used in article):
%
% plotInputResistanceMERGED.m
%
%
clear all, close all
format compact
tic
% Matlab helper scripts are located here
path(path,'../matlabScripts')
% Genesis model is located here
path(path,'../genesisScripts')
nWidth = 5 %2 %5;
numCells = nWidth^3;
pulseDelay = 0.200
pulseDur = 0.200;
nMeasure = 5 %2 %10
nGJvec = 0:2:32; % Number of GJ to check
cellIdx = randperm(numCells)-1;
cellIdx = cellIdx(1:nMeasure); % Use ten random selected neurons
maxTime = (pulseDelay + pulseDur)*length(cellIdx) + pulseDelay;
channelMask = {'A_channel'} % Lägg till fler om fler ska varieras
cellVar = 0.5 % 0.2 % 0.1;
lenVar = 0.5 % 0.2 %0.1;
dataFileMask = 'FSinputResCheck-sec-avgGJ-%d-randSeed-%d.data';
dataDir = 'UTDATA/SAVED/LARGEinputResCheck/SecDend/';
makeFSMorph(numCells, cellVar, channelMask, lenVar)
randSeed = floor(sum(clock)*1e5);
for iGJ=1:length(nGJvec)
disp('Pausing for 3 seconds')
pause(3)
nGJ = nGJvec(iGJ);
clear gapSource gapDest gapRes
% nGJ should be even number
if(nGJ == 0)
gapSource = []; % Reference case
gapDest = []; % Reference case
gapRes = inf; % Reference case, unconnected
else
[gapSource, gapDest, conMat] = ...
makeFSconnectionMatrixOnlySecWrappedSetNGJ(nWidth,nWidth,nWidth,nGJ);
gapRes = ones(length(gapSource),1)*2e9;
conMatFile = sprintf('%sconMat-avgNGap-%d-randSeed-%d.mat', ...
dataDir, nGJ, randSeed);
save(conMatFile, 'conMat');
end
dataFile = sprintf(dataFileMask, nGJ, randSeed);
dataFileGenesis = strrep(dataFile,'.data','');
writeParameters(maxTime,numCells,gapSource,gapDest,gapRes,dataFileGenesis);
for iCell = 1:length(cellIdx)
curStart{iCell} = pulseDelay*iCell + (iCell-1)*pulseDur;
curEnd{iCell} = curStart{iCell} + pulseDur;
curAmp{iCell} = 10e-12; %5e-12;
curLoc{iCell} = sprintf('/fs[%d]/soma', cellIdx(iCell));
end
writeCurrentInputInfo(curStart, curEnd, curAmp, curLoc)
system('genesis ../genesisScripts/simFsMultiInhomogeneCurrentInjection');
infoFile = strrep(dataFile,'.data','.info');
system(sprintf('cp INDATA/parameters.txt UTDATA/%s', infoFile));
system(sprintf('cat INDATA/currentInputInfo.txt >> UTDATA/%s', infoFile));
system(sprintf('mv UTDATA/%s %s', dataFile, dataDir));
system(sprintf('mv UTDATA/%s %s', infoFile, dataDir));
end
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